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A cross-systems primer for synthetic microbial communities

Nature Microbiology volume 9, pages 2765–2773 (2024)Cite this article

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Abstract

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.

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Fig. 1: Dual continuums of ‘question’ and ‘system’ for SynCom research.
Fig. 2: Flow diagram of approaches used when designing, evaluating and deploying a SynCom.
Fig. 3: Examples of bottom–up and top–down design approaches for SynComs.

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Acknowledgements

This manuscript was inspired by an ASM Microbe panel discussion involving many of the authors and organized by the ASM EEB track in 2023. We would like to specifically thank B. Callahan for early discussions on this topic. E.C.M. acknowledges funding from the NSF EAGER award no. 1838299, as well as support from the NSF Postdoctoral Research Fellowships in Biology award no. 2209151. B.K. is a Chan Zuckerberg San Francisco Biohub investigator. B.J. and K.A.P. acknowledge funding from the National Institutes of Health award no. U19 AI157981. G.A. and M.S. were supported by the 3rd Programme for Future Investments (France 2030), operated by the SUCSEED project (ANR- 20- PCPA-0009) and funded by the ‘Growing and Protecting crops Differently’ French Priority Research Program (PPR-CPA), part of the national investment plan operated by the French National Research Agency (ANR). L.P.P.-M. acknowledges funding from Conahcyt (Consejo Nacional de Humanidades, Ciencias y Tecnologías) under awards nos. A1-S-9889 and CBF2023-2024-2642.

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  1. These authors contributed equally: Gontran Arnault, Bishnu Joshi, Laila P. Partida-Martinez and Kathryn A. Patras.

Authors and Affiliations

  1. School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA

    Elijah C. Mehlferber

  2. Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA

    Elijah C. Mehlferber

  3. Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France

    Gontran Arnault & Marie Simonin

  4. Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA

    Bishnu Joshi & Kathryn A. Patras

  5. Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, México

    Laila P. Partida-Martinez

  6. Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA

    Kathryn A. Patras

  7. Department of Integrative Biology, University of California, Berkeley, CA, USA

    Britt Koskella

  8. San Francisco Chan Zuckerberg Biohub, San Francisco, CA, USA

    Britt Koskella

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Contributions

E.C.M. and B.K. developed the framework for the manuscript, with input from all authors. E.C.M. led the writing of the manuscript, with contributions by G.A., B.J., L.P.P.-M., K.A.P., M.S. and B.K. Authors G.A., B.J., L.P.P.-M. and K.A.P. contributed equally to the manuscript; these authors are presented in alphabetical order by surname.

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Mehlferber, E.C., Arnault, G., Joshi, B. et al. A cross-systems primer for synthetic microbial communities. Nat Microbiol 9, 2765–2773 (2024). https://doi.org/10.1038/s41564-024-01827-2

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